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annotate tools/mummer/mummer.py @ 4:5f5a358b281f draft

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v0.0.5 internal changes
author peterjc
date Wed, 05 Aug 2015 11:34:31 -0400
parents 8f93c1b7609e
children 683ea5ab0008
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1 #!/usr/bin/env python
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2 """MUMmer wrapper calling nucmer/promer/mummerplot etc,
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3
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4 Takes the following command line options,
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5 1. FASTA filename of species A
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6 2. FASTA filename of species B
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7 3. Algorithm, nucmer or promer
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8 4. PNG output filename
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9 5. PDF output filename
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10 """
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11
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12 import os
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13 import sys
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14 import tempfile
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15 import shutil
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16
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17 def sys_exit( msg ):
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18 sys.stderr.write("%s\n" % msg)
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19 sys.exit(1)
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21 def run(cmd):
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22 print(cmd)
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23 return_code = os.system(cmd)
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24 if return_code:
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25 sys_exit("Error %i from: %s" % (return_code, cmd))
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27 if "-v" in sys.argv [1:]or "--version" in sys.argv[1:]:
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28 print("MUMmer wrapper v0.0.3\n")
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29 # TODO - How to get a version string from the mummer binary?
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30 os.system("nucmer --version")
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31 os.system("promer --version")
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32 os.system("mummerplot --version")
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33 sys.exit(0)
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35 #Parse Command Line
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36 #TODO - optparse
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37 try:
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38 fasta_a, fasta_b, algorithm, png_out, pdf_out = sys.argv[1:]
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39 except:
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40 sys_exit("Expect 5 arguments, got %i" % (len(sys.argv) - 1))
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43 valid_algo = ["mummer", "nucmer", "promer"]
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44 if algorithm not in valid_algo:
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45 sys_exit("Invalid algorithm argument %r, should be: %s" % (algorithm, ", ".join(valid_algo)))
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47 base_path = tempfile.mkdtemp()
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48 prefix = os.path.join(base_path, "ref_qry")
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49 coords = prefix + ".mums"
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50 #gnuplot = prefix + ".gp"
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51 ps_image = prefix + ".ps"
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52 png_image = prefix + ".png"
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54 if algorithm == "mummer":
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55 #Add -mum as per example to find maximal unique matches between ref and query.
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56 #Add the -b -c options to search both strands and report relative to forward strand
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57 #which then matches the default dual-strand approach in nucmer and promer
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58 cmd = '%s -mum -b -c "%s" "%s" > %s' % (algorithm, fasta_a, fasta_b, coords)
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59 else:
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60 coords = "out.delta"
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61 cmd = '%s "%s" "%s"' % (algorithm, fasta_a, fasta_b)
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62 run(cmd)
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63
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64 # PNG
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65 # ===
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66 cmd = 'mummerplot -R "%s" -Q "%s" --png --large --prefix=%s %s' % (fasta_a, fasta_b, prefix, coords)
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67 run(cmd)
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68 shutil.move(png_image, png_out)
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70 # PS --> PDF
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71 # ==========
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72 # Using --large, puts "set size 3,3" in the gnuplot - which seems to mess up.
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73 # Problem here is the default bbox (BoundingBox) in the PS output is letter page size,
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74 # and even if we override that, at least when view the PS output in Adobe Illustrator
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75 # things don't seem to be lined up properly :(
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76 #
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77 # Using "set size 1,1" works better - which is what --small gives:
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78 cmd = 'mummerplot -R "%s" -Q "%s" --postscript --small --prefix=%s %s' % (fasta_a, fasta_b, prefix, coords)
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79 run(cmd)
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80 cmd = 'ps2pdf -dEPSCrop "%s" "%s"' % (ps_image, pdf_out)
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81 run(cmd)
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82
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83 #Remove temp files...
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84 os.remove(coords) # Might not be under the temp directory...
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85 shutil.rmtree(base_path)